* Topology for water and ions
*
31  1

MASS  -1  HT         1.00800 H ! TIPS3P WATER HYDROGEN
MASS  -1  HX         1.00800 H ! hydroxide hydrogen
MASS  -1  OT        15.99940 O ! TIPS3P WATER OXYGEN
MASS  -1  OX        15.99940 O ! hydroxide oxygen
MASS  -1  LIT        6.94100 LI ! Lithium ion
MASS  -1  SOD       22.98977 NA ! Sodium Ion
MASS  -1  MG        24.30500 MG ! Magnesium Ion
MASS  -1  POT       39.09830 K ! Potassium Ion
MASS  -1  CAL       40.08000 CA ! Calcium Ion
MASS  -1  RUB       85.46780 RB ! Rubidium Ion
MASS  -1  CES      132.90545 CS ! Cesium Ion
MASS  -1  BAR      137.32700 BA ! Barium Ion
MASS  -1  ZN        65.37000 ZN ! zinc (II) cation
MASS  -1  CAD      112.41100 CD ! cadmium (II) cation
MASS  -1  CLA       35.45000 CL ! Chloride Ion

default first none last none

RESI TIP3         0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2  OT     -0.834
ATOM H1   HT      0.417
ATOM H2   HT      0.417
BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shake
ANGLE H1 OH2 H2             ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

RESI TP3M         0.000 ! "mmff" water model, as an analog of tip3p
GROUP
ATOM OH2  OT     -0.834 ! these charges are replaced by the mmff setup
ATOM H1   HT      0.417 ! these charges are replaced by the mmff setup
ATOM H2   HT      0.417 ! these charges are replaced by the mmff setup
BOND OH2 H1 OH2 H2      ! omits the H1-H2 bond, which is needed for shake with tip3p
ANGLE H1 OH2 H2         ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

RESI OH       -1.00 ! hydroxide ion by adm.jr.
GROUP
ATOM O1 OX    -1.32
ATOM H1 HX     0.32
BOND O1 H1
DONOR H1 O1
ACCEPTOR O1

! Ion parameters from Benoit Roux and Coworkers
! As of 8/10 new NBFIX terms required
!
RESI LIT       1.00 ! Lithium Ion
GROUP
ATOM LIT  LIT  1.00
PATCHING FIRST NONE LAST NONE

RESI SOD       1.00 ! Sodium Ion
GROUP
ATOM SOD  SOD  1.00
PATCHING FIRST NONE LAST NONE

RESI MG        2.00 ! Magnesium Ion
GROUP
ATOM MG   MG   2.00
PATCHING FIRST NONE LAST NONE

RESI POT       1.00 ! Potassium Ion
GROUP
ATOM POT   POT 1.00
PATCHING FIRST NONE LAST NONE

RESI CAL       2.00 ! Calcium Ion
GROUP
ATOM CAL  CAL  2.00
PATCHING FIRST NONE LAST NONE

RESI RUB       1.00 ! Rubidium Ion
GROUP
ATOM RUB  RUB  1.00
PATCHING FIRST NONE LAST NONE

RESI CES       1.00 ! Cesium Ion
GROUP
ATOM CES  CES  1.00
PATCHING FIRST NONE LAST NONE

RESI BAR       2.00 ! Barium Ion
GROUP
ATOM BAR  BAR  2.00
PATCHING FIRST NONE LAST NONE

RESI ZN2       2.00 ! Zinc (II) cation, Roland Stote
GROUP
ATOM ZN   ZN   2.00
PATCHING FIRST NONE LAST NONE

RESI CD2       2.00 ! Cadmium (II) cation
GROUP
ATOM CD   CAD  2.00
PATCHING FIRST NONE LAST NONE

RESI CLA      -1.00 ! Chloride Ion
GROUP
ATOM CLA  CLA -1.00
PATCHING FIRST NONE LAST NONE

END
